General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)
General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)
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DOI：
10.3389/fmars.2020.00225
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发表时间：
2020-01
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影响因子：
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通讯作者：
Yaamini R. Venkataraman;Alan M. Downey‐Wall;J. Ries;I. Westfield;S. White;S. Roberts;K. Lotterhos
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文献类型：
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作者：
Yaamini R. Venkataraman;Alan M. Downey‐Wall;J. Ries;I. Westfield;S. White;S. Roberts;K. Lotterhos
表观遗传修饰，特别是DNA甲基化，是代际可塑性的一种可能机制。在对甲基化模式的遗传进行表征之前，我们需要更好地了解环境变化如何改变亲本表观基因组。为研究实验性海水酸化对东方牡蛎性腺组织的影响，在实验室内分别在pCO2控制（491 ± 49 μatm）和高（2550 ± 211 μatm）的条件下进行了为期4周的养殖。从生殖组织中分离出的DNA从五个牡蛎每次治疗，然后进行亚硫酸氢盐处理和DNA测序。不考虑处理，DNA甲基化主要在基因体中发现，C. virginica基因组被甲基化。在pCO2升高的反应中，我们发现598个差异甲基化位点主要与基因体重叠。大部分差异甲基化位点位于外显子（61.5%），内含子重叠较少（31.9%）。虽然没有证据表明具有差异甲基化位点的基因与不同的生物过程相关的显着趋势，但这些位点在基因体中的浓度，包括参与蛋白质泛素化和生物矿化的基因，表明DNA甲基化可能对响应海洋酸化的转录控制很重要。性腺甲基化的变化也表明这些甲基化模式有可能被后代遗传。了解实验性海洋酸化条件如何修改牡蛎表观基因组，以及这些修改是否遗传，可以更好地了解生态系统如何应对环境变化。
Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 μatm) or high (2550 ± 211 μatm) pCO2 conditions for four weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of CpGs (2.7% of total cytosines) in the C. virginica genome predicted to be methylated. In response to elevated pCO2, we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Changes in gonad methylation also indicate potential for these methylation patterns to be inherited by offspring. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change.